[Eeglablist] Why most of good 'brain' ICs are 'dipolar' with show 'red'-centerd scalp topos, although 2/3 of the cortex is in sulci?

[Makoto Miyakoshi]

Dear Ramesh,

> Suppose there is a phase difference between two adjacent gyri.  There
will be some cancellation of signal but there will still be more signal
than if only 1 gyrus was active except for the 180 degree out of phase
case.

Hmm I think I understood your point. It took me time, but I remembered the
rather shocking but theoretically not surprising visualizations and a
conclusion from this study.
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1053811916301884__;!!Mih3wA!G_Ojrd8F7PZfZkuwWzWgsS0JVHvWMtrSgPfLywQuwpNYVzbJPo15amBcOKX7xf3omORoWs_YmMlVXxKDyaSj_3wb_t4$ 

Their conclusion even applies to the case of ICA-derived 'sources'. After
all, it's not the unitary phases across cortical columns, but it is 'a'
spatially fixed repeating pattern of a phase configuration that is
necessary to form a 'dipolar' scalp projection.

Makoto


On Wed, Dec 13, 2023 at 10:33 PM Ramesh Srinivasan <srinivar at uci.edu> wrote:

> Makoto
>
> I think Paul's intent was specifically to challenge the thalamocortical
> account in humans.
>
> I want to point out one other thing I noticed in the discussion going back
> to Scott and your comments
>
> The idea that the lag zero synchrony is a requirement over the cortex is
> often used to justify the thalamocortical account.
>
> I don't think we need that at all. Suppose there is a phase difference
> between two adjacent gyri.  There will be some cancellation of signal but
> there will still be more signal than if only 1 gyrus was active except for
> the 180 degree out of phase case.
>
> In this scenario different scalp electrodes will show different phases
> which can be observed in many papers.
>
> Ramesh Srinivasan
> Professor
> Cognitive Sciences
> Biomedical Engineering
>
> On Wed, Dec 13, 2023, 5:16 PM Makoto Miyakoshi via eeglablist <
> eeglablist at sccn.ucsd.edu> wrote:
>
>> Thanks Pål for your comments.
>> I don't think many people believe the thalamus==pacemaker hypothesis any
>> more.
>> Lopes da Silva found high coherence between dog's visual cortex and
>> pulvinar instead of LGN in his 1980 paper. Saalmann et al. (2012) was a
>> nice confirmation of that using monkeys. Basically, they identified the
>> pulvinar-V4/TEO (i.e. thalamo-cortical) network of the active visual
>> attention. Such a network is 'recruited' upon top-down demand, perhaps as
>> a
>> part of a larger network.
>>
>> Although Nunez insisted on the presence of traveling and standing waves, I
>> do not think his claim was to replace the conventional alpha models.
>> Instead, such a network can be present on top of something else. I agree
>> with you that his claim was 'more or less shot down' except no one dared
>> to
>> shoot it but it has been unattended. But you know, Alex Fornito's the
>> Nature paper in the early 2023 is nothing but fMRI version of Nunez's
>> global field theory with less explanation. They could not explain what
>> exactly is traveling in their model. In the case of Nunez's model, the
>> medium of the traveling wave is clear: the synaptic action fields mediated
>> by white matters.
>>
>> > 3. The amplitudes of EEG will be linear to the number of synchronous
>> firing neurons. If they are firing stochasticly the amplitude will be
>> closer to the square root. E.g. 1000000 neurons will in synchrony give an
>> unite amplitude of 1000000 as if they have a stochastic firing 1000.
>> Coherences gives amplitudes somewhere in between.
>>
>> I made a humble plot from this simulation. If you are curious, please see
>> slide 49 linked below. Basically, after passing some critical point, the
>> small-number synchronous firing effect start to outweigh the mass random
>> firing effect. It's a replication of Hari et al. (1997).
>>
>> https://urldefense.com/v3/__https://sccn.ucsd.edu/mediawiki/images/1/13/On_EEG*27s_generative_mechanism.pdf__;JQ!!CzAuKJ42GuquVTTmVmPViYEvSg!ICVjAWd2SZrqFNUJPogEQBLx6o5k3xGNW-hHxSnaf7aCYHU_zo4Jt_XjJOIJCHBOxtCMaVK2EfXI7J-oMMrUGQ00$
>>
>> In the actual 3-D implementation of the sheet of (a massive number of)
>> parallel pyramidal neurons, there is also a counter-intuitive non-linear
>> spatial summation effect. I call it a transducer array effect. This also
>> favors the wide EEG sources to be scalp-recorded. The explanation is lined
>> below.
>>
>> https://urldefense.com/v3/__https://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline*Transducer_array_effect_.28For_140.2C000_page_views.2C_10.2F09.2F2020_added.29__;Iw!!CzAuKJ42GuquVTTmVmPViYEvSg!ICVjAWd2SZrqFNUJPogEQBLx6o5k3xGNW-hHxSnaf7aCYHU_zo4Jt_XjJOIJCHBOxtCMaVK2EfXI7J-oMDXc1K8M$
>>
>> > 2. The nature is not redundant in the way that many neurons are used for
>> the same function. You will not expect close by neurons to be in
>> synchrony.
>> Why should they? But there will be coherent elements.
>>
>> Right. I think the point is sparsity and efficiency.
>> For example, we might think 1% of synchrony is trivial. But most of the
>> esoteric cognitive neuroscience studies rely on BOLD signal measurement
>> that shows changes often less than 1%.
>> I think when samples are ample, a small fraction of changes still counts.
>>
>> Speaking of the global field theory, when I asked Paul Nunez what
>> he thought of the view by Buszaki that frequencies of the brain rhythm are
>> stable across species, he immediately disagreed. I would love to
>> see someone replicate Buszaki's claim there.
>>
>> Makoto
>>
>> On Wed, Dec 13, 2023 at 12:10 PM Pål Gunnar Larsson <pall at ous-hf.no>
>> wrote:
>>
>> > Hi Makoto
>> >
>> > I hope I did not open Pandoras box. First a small history.
>> > Andersen and Andersson publish in 1968 that alpha activity came from
>> > pacemaker cells in Thalamus. This was a cat study. In 1971 Sturm van
>> Leuwen
>> > and Lopez da Silva showed in dog that there were no good coherence
>> between
>> > the thalamus activity and the alpha. Even the frequencies didn’t match.
>> > Then Nunez suggested alpha was generated by standing waves in cortex
>> with
>> > some human data. However, also his hypothesis was more or less shot
>> down.
>> > Now, it seems like a leading hypothesis is that alpha is generated by
>> > cortical spreading activity that to some extend is influenced by
>> standing
>> > waves. My point here is that model and methods to a large extend
>> influences
>> > your results.
>> >
>> > Let me make some points
>> > 1. Propagating takes time, hence you get a phase shifted as a function
>> of
>> > distance in cortex. This will give cancellations in the EEG due to the
>> > spatial averaging. Therefore our electrodes "sees" patchy activity.
>> > 2. The cortico-cortical fibers propagate AP with up to 9 m/s and
>> > intracortical propagation is 0.2m/s- 0.5 m/s.
>> > 2. The nature is not redundant in the way that many neurons are used for
>> > the same function. You will not expect close by neurons to be in
>> synchrony.
>> > Why should they? But there will be coherent elements.
>> > 3. The amplitudes of EEG will be linear to the number of synchronous
>> > firing neurons. If they are firing stochasticly the amplitude will be
>> > closer to the square root. E.g. 1000000 neurons will in synchrony give
>> an
>> > unite amplitude of 1000000 as if they have a stochastic firing 1000.
>> > Coherences gives amplitudes somewhere in between.
>> > 4. The EEG we record are to a large extend from not highly correlated
>> > neurons with coherences waxing and waning depending on the activity.
>> E.g.
>> > Evoked potentials gives higher coherences and hence, higher amplitudes.
>> > 5. Thalamus is an important relay station in the brain, but I am not
>> > convinced that it has an important pacemaker function, at least not in
>> > humans.
>> > 6. I think I have to go back to the PL Nunez book to find his references
>> > on the human vs rodent brain wiring.
>> >
>> > To me the EEG is mostly modulated by changing activities in the brain
>> and
>> > not by some pacemakers.
>> >
>> > Best
>> > Pål
>> >
>> > E-mail: pall at ous-hf.no
>> >
>> > Ikke sensitiv
>> >
>> > -----Opprinnelig melding-----
>> > Fra: eeglablist <eeglablist-bounces at sccn.ucsd.edu> På vegne av Makoto
>> > Miyakoshi via eeglablist
>> > Sendt: 12. desember 2023 19:35
>> > Til: eeglablist <eeglablist at sccn.ucsd.edu>
>> > Emne: Re: [Eeglablist] Why most of good 'brain' ICs are 'dipolar' with
>> > show 'red'-centerd scalp topos, although 2/3 of the cortex is in sulci?
>> >
>> > Hi Pal and Ramesh,
>> >
>> > Thank you for your comments.
>> > Let me quote an explanation from Jones (2002) "Thalamic circuitry and
>> > thalamocortical synchrony" p.1669. He explains how the two types of
>> > thalamocortical projections, core and matrix, interact to create
>> cortical
>> > activities, which is probably the direct source of EEG/MEG signals.
>> >
>> > %%%%%%%%%%%%%%%%%
>> > The relay cells of the thalamic core, with their focused projections to
>> an
>> > individual cortical area, clearly form the basis for the relay of place-
>> > and modality-specific information to the cortex whereas those of the
>> > thalamic matrix form a more obvious basis for the dispersion of
>> activity in
>> > the thalamocortical network across larger areas of cortex. Within a
>> zone of
>> > cortex, the terminations of matrix cell axons on distal dendrites in
>> > superficial layers and of matrix cell axons on more proximal dendrites
>> in
>> > middle layers should serve as a coincidence detection circuit, providing
>> > for a high degree of temporal integration between inputs coming from the
>> > two classes of thalamic cells (Llinas&Pare 1997; figure 11).
>> Coincidence of
>> > this kind should promote synchronous activity in the cells of individual
>> > cortical columns and in any group of columns activated by the same
>> > stimulus. Activity in these columns would then be returned via layer VI
>> > corticothalamic cells to the thalamic nucleus from which they receive
>> > input, serving  to reinforce thalamocortical synchrony. This activity
>> would
>> > be spread to other cortical columns in the same cortical area and in
>> > adjacent cortical areas via the diffuse projections of matrix cells in
>> the
>> > thalamic nucleus through which externally or internally generated
>> activity
>> > was first passed to the cortex.
>> > %%%%%%%%%%%%%%%%%
>> >
>> > I guess fMRI-based 'functional mapping' is rather close to the mapping
>> of
>> > the projections by 'core thalamic nuclei'.
>> >
>> > When I analyzed the USCD mismatch negativity (MMN) database, I found MMN
>> > is a whole-brain phenomenon and not limited to Fz. One of the coauthors
>> > (probably Juan) asked me why the 'visual cortex' showed ERP as well. I
>> > could not answer to his question. Now I have a better explanation--From
>> the
>> > core/matrix point of view, it is not surprising that auditory stimulus
>> > activates cortices of other sensory modalities.
>> >
>> > Giandomenico Ianetti from U Rome showed me 4 or 5 ERPs evoked by stimuli
>> > of different modalities including visual, auditory, tactile, and
>> > laser-evoked pain. His point was clear: These ERPs are the same. It was
>> > eyes opening.
>> >
>> > So, this is my proposal: Let us unlearn the fMRI-based functional brain
>> > mapping when we do EEG. Instead, let us pay more attention to thalamus.
>> >
>> > I do not know about the cortico-cortical connection via u fiber very
>> much.
>> > If you know a paper detailing that point, please let me know. My initial
>> > respose is, is the u-fiber connection fast enough to form a
>> > near-simultaneous activity across the cortex? Isn't a region-wide
>> > projection from the thalamus more feasible to explain it?
>> >
>> > Makoto
>> >
>> >
>> > On Tue, Dec 12, 2023 at 12:25 PM Ramesh Srinivasan via eeglablist <
>> > eeglablist at sccn.ucsd.edu> wrote:
>> >
>> > > I've been enjoying this discussion because it taps into one of those
>> > > EEG truths/inconsistencies we never talk about.
>> > >
>> > > 1. We artifact edit EEG data mostly based on the idea it should be
>> > > smooth low spatial frequency information.  We don't trust very
>> > > (channel, frequency, time)  localized EEG signals.
>> > >
>> > > 2. Then after we clean the EEG data we want a story for our paper that
>> > > is time, frequency, source localized as compact as possible because it
>> > > makes a nice narrative.
>> > >
>> > > Regarding synchrony in adjacent gyri, u-fibers are helpful and yes, I
>> > > think most of it is corticocortical rather than thalamocortical but I
>> > > think the 2% is just a guess. It's clearly not as thalamocortical as
>> > > animal models
>> > >
>> > > Ramesh Srinivasan
>> > > Professor
>> > > Cognitive Sciences
>> > > Biomedical Engineering
>> > >
>> > > On Tue, Dec 12, 2023, 6:40 AM Pål Gunnar Larsson via eeglablist <
>> > > eeglablist at sccn.ucsd.edu> wrote:
>> > >
>> > > > Just want to add. In rats about 50% of all fiber going in and out of
>> > > > the cortex are connected to the thalamus. In humans connections are
>> > > > about 2%, according to Nunez. Hence, we should be very careful when
>> > > > you try to extrapolate from animal research to humans.
>> > > >
>> > > > Pål G. Larsson
>> > > >
>> > > > Ikke sensitiv
>> > > >
>> > > >
>> > > > -----Opprinnelig melding-----
>> > > > Fra: eeglablist <eeglablist-bounces at sccn.ucsd.edu> På vegne av
>> > > > Makoto Miyakoshi via eeglablist
>> > > > Sendt: 11. desember 2023 19:06
>> > > > Til: EEGLAB List <eeglablist at sccn.ucsd.edu>
>> > > > Emne: Re: [Eeglablist] Why most of good 'brain' ICs are 'dipolar'
>> > > > with show 'red'-centerd scalp topos, although 2/3 of the cortex is
>> in
>> > sulci?
>> > > >
>> > > > Hi Scott,
>> > > >
>> > > > > "How are LFP signals across each of these gyrii synchronized
>> > > > > across the
>> > > > dataset?"
>> > > >
>> > > > The answer is not so special. The synchrony is achieved via
>> > > > thalamo-cortical loops.
>> > > > In the following Wiki article, I linked to my presentation at an NIH
>> > > > summer seminar in which I showed multiple evidence that cortical
>> > > synchrony
>> > > > and coupling is controlled by thalamus.
>> > > >
>> > > >
>> > >
>> https://urldefense.com/v3/__https://sccn.ucsd.edu/wiki/Makoto*27s_prep
>> > > rocessing_pipeline*Two_presentations_at_a_seminar:_EEG_preprocessing_a
>> > > nd_generative_mechanism_.28For_240.2C000_page_views.2C_09.2F21.2F2023_
>> > > added.2C_10.2F18.2F2023_updated.29__;JSM!!CzAuKJ42GuquVTTmVmPViYEvSg!I
>> > > xfdnbB611_BrP_68EFD1xVZHKoKQu6E2vLO7VJL104Il5HhWcGfwu-K0btGTDMoDcUuo0-
>> > > 5NDYMK30iA7NCfDue$
>> > > >
>> > > > So, when thalamus makes different cortical regions to fire together,
>> > > > then you see the synchronous activity. That's it. The distant
>> > > > cortical regions do not have to be directly connected via each
>> > > > neuron's lateral branches (which does exist, but the conduction
>> > > > speed is very slow compared with
>> > > that
>> > > > of white matter) Note this is not a one-way 'imposing' the rhythm
>> > > > from
>> > > the
>> > > > thalamus to the cortex, like the historical 'pace-maker' hypothesis
>> > > > by Andersen and Andersen (1967) but it is a bi-directional
>> interaction.
>> > > >
>> > > > One fact that might help you see the situation is that only 1% of
>> > > > neurons need to be synchronized to form 95% of the amplitude of the
>> > > > observed
>> > > signal
>> > > > according to Hari (1997).
>> > > >
>> > > > Also, it might also help to remember that there is no general
>> > > > guarantee that an EEG source is stationary and localizable. See
>> > > > Izhikevich's classical simulation.
>> > > >
>> > > >
>> > >
>> https://urldefense.com/v3/__https://www.izhikevich.org/publications/la
>> > > rge-scale_model_of_human_brain.htm__;!!Mih3wA!FLAtrGcNSxCRup1LcnfgWIJk
>> > > dfC5HMOr_rPujEIjdmGug69GeOA7PxjXg5NqsRrbtx3VtKZRJhKrQ9HIAFxdjg0n5Fg$
>> > > > There is an established principle of functional brain mapping but it
>> > > > is a product of statistical processing such as (heavy) averaging.
>> > > > ICA model is the same, hence it is stationary across time. The small
>> > > > and localizable
>> > > EEG
>> > > > source is heavily a statistical concept. The actual ongoing EEG is
>> > > > stochastic, dynamic, and diffuse. When we see ICA results,
>> > > > therefore, we should distinguish properties of the filter from
>> > properties of data.
>> > > >
>> > > > Makoto
>> > > >
>> > > >
>> > > > On Mon, Dec 11, 2023 at 11:42 AM Scott Makeig <smakeig at gmail.com>
>> > wrote:
>> > > >
>> > > > > Makoto -
>> > > > >
>> > > > > When you repeat the claim that EEG sources 'found' by ICA
>> > > > > decomposition must be at least several adjacent gyrii in size, you
>> > > > > fail to ask, "How are LFP signals across each of these gyrii
>> > > > synchronized across the dataset?"
>> > > > > Doesn't this require some physiological basis, and if so, what is
>> > it??
>> > > > >
>> > > > > Scott Makeig
>> > > > >
>> > > > > On Mon, Dec 11, 2023 at 11:17 AM Makoto Miyakoshi via eeglablist <
>> > > > > eeglablist at sccn.ucsd.edu> wrote:
>> > > > >
>> > > > >> Hello EEGLAB list,
>> > > > >>
>> > > > >> For those who have wondered so, here are my answers.
>> > > > >> I asked two questions:
>> > > > >>
>> > > > >> (1) Why do good 'brain' ICs show dipolar scalp topos although 2/3
>> > > > >> of the cortex is in sulci?
>> > > > >> (2) Why do these dipolar IC scalp topos show red (positive)
>> centers?
>> > > > >>
>> > > > >> The answer was published a few days ago.
>> > > > >>
>> > > > >>
>> > > > >>
>> https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/1
>> > > > >> 0.10
>> > > > >> 02/hbm.26540__;!!Mih3wA!FPOThEiX2hsD7TJBq7WyhlV8v6HSkTe_swsBEoB2R
>> > > > >> M-Bh -BGerduzZBnmEtDBamyosThbqv9Xrc1gGPSmdm52LpO7jM$
>> > > > >>
>> > > > >> The answer to (1): It is because scalp-recorded EEG is
>> > > > >> insensitive to sulcal sources compared with gyral sources. This
>> > > > >> finding justifies the use of lissencephalic (i.e. no sulci) brain
>> > > > >> model proposed in Electric Fields of the Brain (Nunez and
>> > > > >> Srinivasan, 2006) together
>> > > with
>> > > > Spline Laplacian.
>> > > > >> This also supports the view that the major source of
>> > > > >> scalp-recordable EEG is pretty broad (minimum 6.45 cm^2) which
>> > > > >> requires a continuum of multiple gyral crowns.
>> > > > >>
>> > > > >> I did not write it in the paper, but the result basically refutes
>> > > > >> the claim that ICA is a high-resolution EEG spatial filter
>> > > > >> because the result confirms that ICA is mostly blind to 2/3 of
>> > > > >> the cortex. In fact, it seems ICA results are always dominated by
>> > > > >> high-power, low-frequency, and very broad sources. I will publish
>> > > > >> this view in the near future.
>> > > > >>
>> > > > >> The answer to (2): It is because EEGLAB's ICA sets the initial
>> > > > >> topos of all ICs red centered (i.e. positive dominant). Thus,
>> > > > >> unless necessary, the algorithm does not flip the polarities.
>> > > > >>
>> > > > >> Now you wonder--when does the ICA algorithm flip the polarity to
>> > > > >> produce 'blue' centered (i.e. negative dominant) ICs? I found
>> > > > >> that those blue-centered ICs tend to show poor physiological
>> > > > >> validity with large index numbers. A known clear exception for
>> > > > >> this rule is ICs localized for the motor cortex.
>> > > > >>
>> > > > >> People use ICA to clean EEG. I use EEG to glean ICA, which is
>> > > > >> more
>> > > fun.
>> > > > >>
>> > > > >> Makoto
>> > > > >> _______________________________________________
>> > > > >> Eeglablist page:
>> > > >
>> > >
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>> > > > >
>> > > > >
>> > > > > --
>> > > > > Scott Makeig, Research Scientist and Director, Swartz Center for
>> > > > > Computational Neuroscience, Institute for Neural Computation,
>> > > > > University of California San Diego, La Jolla CA 92093-0559,
>> > > > >
>> > > >
>> > >
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>> > > > >
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